Fructan vs. gluten intolerance

“Gluten is the problem.” It’s a phrase registered dietitian nutritionists (RDNs) hear often. Gluten is frequently assumed to be the trigger when gastrointestinal symptoms arise after wheat consumption. However, emerging research suggests that the wrong culprit is being targeted. In many cases, the true driver of symptoms is not gluten, but fructans, a naturally occurring carbohydrate found in wheat, garlic, onions, and a variety of other everyday foods. 

Fructans aren’t inherently harmful. In fact, they serve as prebiotics, feeding beneficial gut bacteria. But in sensitive individuals, they can ferment in the gut, leading to bloating, gas, and changes in bowel habits. 

Understanding the difference between gluten and fructan intolerance helps explain why some patients see little improvement on a gluten-free diet. Symptoms may persist despite avoiding gluten, suggesting the need for a more targeted approach. And for some, removing gluten unnecessarily can lead to overly restrictive eating patterns. 

This blog will explore what fructans are, how they affect digestion, why symptoms often overlap with gluten sensitivity, and how to identify the true source of your patient’s discomfort.  

Understanding fructans: Structure and physiological impact 

Fructans are complex carbohydrates composed of fructose chains. These polymers of fructose units are linked by β (2-1) glycosidic bonds, classified by chain length into two primary categories: 

• Fructo-oligosaccharides (FOS): Short-chain polymers containing 2-9 fructose units 
• Inulins: Long-chain polymers containing 10-60 fructose units  

Fructans are naturally occurring prebiotic fibers found in diverse food categories: 

• Cereal grains: wheat, rye, barley  
• Vegetables: onions, garlic, leeks, asparagus, Jerusalem artichokes  
• Fruits: ripe bananas, watermelon, nectarines  
• Legumes: selected varieties including lentils and chickpeas 

Human digestive enzymes lack the capacity to hydrolyze fructan polymers. Consequently, these compounds transit undigested through the small intestine to the colon, where resident microbiota ferment them through anaerobic metabolism. This fermentation process produces short-chain fatty acids, gases (hydrogen, methane, carbon dioxide), and increases luminal osmotic load, potentially triggering gastrointestinal symptoms in susceptible individuals.  

Differential diagnosis: Gluten vs. fructan sensitivity 

While celiac disease affects only approximately 1% of the United States population, a higher rate follows a gluten-free diet for symptom management. This discrepancy suggests many may be unnecessarily avoiding gluten when fructan intolerance could be the true cause. 

The growing body of evidence indicating fructans as the primary trigger in many cases of presumed gluten sensitivity has significant implications for clinical management. Patients who improve on gluten-free diets may be inadvertently following a lower fructan diet, as many high-gluten foods are also high in fructans. 

Symptom overlap 

Gluten sensitivity and fructan intolerance share a very similar symptom profile, complicating diagnosis. This overlap is largely due to wheat’s dual composition: it contains both gluten proteins and fructan carbohydrates. Without careful evaluation, symptoms may be misattributed, leading to overly restrictive diets that limit more than necessary. 

Prevalence and diagnostic considerations 

• Celiac disease: Has well-established diagnostic criteria, including serology and histological confirmation via duodenal biopsy showing villous atrophy. 
• Non-celiac gluten sensitivity: A less well-defined condition with up to 6% of Americans experiencing non-celiac gluten sensitivity. Diagnosis remains largely exclusionary, requiring negative celiac serology and biopsy with symptom improvement on a gluten-free diet. 
• Fructan intolerance: Emerging recognition as a distinct clinical entity with particular relevance in functional gastrointestinal disorders. Diagnosis typically involves hydrogen breath testing (although its accuracy is limited) or systematic elimination and reintroduction protocols. 

Diagnostic differentiation strategies 

The challenge lies in distinguishing between these conditions when wheat consumption triggers symptoms. Clinical assessment should consider: 

• Symptom response patterns: Reactions to gluten-free, fructan-containing foods suggest fructan sensitivity rather than gluten intolerance. Improved tolerance to sourdough bread despite gluten presence may indicate fructan intolerance. Spelt sourdough contains minimal fructans while retaining gluten, making it possibly useful as a diagnostic tool. 
• Systematic food challenges: Sequential testing of isolated gluten and fructan sources can help differentiate sensitivities.  

Clinical examples 

• Fructan-specific reactions: Garlic and onions are gluten-free yet high in fructans, often triggering bloating, cramping, and gas in sensitive individuals 
• Fermentation effects: Traditional sourdough fermentation reduces fructan content while retaining gluten. This may explain why some people tolerate sourdough but react to standard bread. 

For example, a patient who reacts to garlic and onions but tolerates spelt sourdough likely has fructan intolerance, not gluten sensitivity. 

Fructan intolerance in irritable bowel syndrome 

Multiple controlled studies have demonstrated that fructans, rather than gluten, may be the primary trigger for gastrointestinal symptoms in individuals with IBS who report gluten sensitivity: 

• Biesiekierski et al. (2013): In a landmark study, participants with reported non-celiac gluten sensitivity consumed a low FODMAP diet for two weeks and then went through a challenge period with either a high gluten, low gluten, or placebo diet. While all participants experienced symptom improvement during the low FODMAP period, no gluten-specific effects were observed during the gluten challenge phases. 

• Skodje et al. (2018): A Norwegian study provided 59 patients with self-reported gluten sensitivity with muesli bars containing gluten, fructans, or a placebo. Results demonstrated that fructans caused significantly worse gastrointestinal symptoms compared to gluten, with symptom severity comparable between gluten and placebo groups. 

• Recent controlled trials: Additional research has shown that when IBS patients consume meals high in FODMAPs versus high in gluten (with a background diet low in both), FODMAPs consistently worsen gastrointestinal symptoms while gluten shows no significant difference from placebo. 

Low FODMAP diet and fructan intolerance  

The low FODMAP diet, developed at Monash University, offers a structured, evidence-based approach for managing fructan intolerance and other FODMAP-related sensitivities. It is particularly effective for individuals with irritable bowel syndrome (IBS). 

FODMAP stands for “fermentable oligosaccharides, disaccharides, monosaccharides, and polyols,” which are short-chain carbohydrates that are poorly absorbed in the small intestine and rapidly fermented in the colon, often leading to gas, bloating, and other gastrointestinal symptoms. 

The main FODMAP subgroups include: 

• Oligosaccharides: Fructans and galacto-oligosaccharides (GOS), found in wheat, rye, garlic, onions, legumes, and some nuts. 
• Disaccharides: Lactose, found in milk and dairy products. 
• Monosaccharides: Excess fructose, found in fruits such as apples, pears, and mangoes. 
• Polyols: Sugar alcohols like sorbitol, mannitol, erythritol, and xylitol, found in certain fruits, vegetables, and sugar-free products. 

The diet is implemented in three phases: 

• Elimination: Temporary removal of all high-FODMAP foods for 2–6 weeks to reduce symptoms. 
• Reintroduction: Gradual reintroduction of individual FODMAP groups to identify personal triggers. 
• Personalization: Development of a long-term eating plan tailored to the individual’s tolerance levels, ensuring variety and nutritional balance. 

While the low FODMAP diet is effective in managing symptoms, especially in IBS, studies show it can reduce populations of beneficial gut bacteria, particularly Bifidobacteria. This potential impact on the gut microbiome highlights the importance of professional supervision and thoughtful reintroduction to support long-term digestive health. 

Galacto-oligosaccharides and combined intolerance 

Some foods contain a combination of several FODMAPs. A common example is the presence of both fructans and galacto-oligosaccharides (GOS) in foods like cashews and red kidney beans. For individuals with sensitivities to multiple FODMAPs, following the low FODMAP diet and then reintroducing foods that are high in only one type of FODMAP at a time can help identify specific intolerances and guide more personalized dietary recommendations. 

Evidence-based clinical recommendations 

Effective management of fructan intolerance requires a systematic, evidence-based approach by RDNs that prioritizes precision over broad dietary restrictions. This comprehensive protocol integrates assessment, intervention, and ongoing monitoring strategies to achieve optimal clinical outcomes while maintaining nutritional adequacy and dietary variety. 

Log diet and GI symptoms  

Patients may benefit from the use of diet logs to document specific gastrointestinal symptoms and their relationship to food intake. This practice can help increase awareness of fructan consumption patterns and individual tolerance levels.

Encourage tracking of symptom severity, timing, and duration in relation to specific foods and meal compositions to help identify personalized triggers. However, avoid recommending food and symptom logging to individuals at risk for or currently experiencing eating disorders. 

Targeted fructan reduction  

Instead of broadly eliminating gluten, focus on identifying and systematically reducing high-fructan foods. Assess individual tolerance, as some clients may handle small amounts or occasional intake without worsening symptoms. Begin by limiting foods with the highest fructan content, while aiming to preserve overall dietary variety and nutritional adequacy. 

Low FODMAP protocol implementation  

A structured, time-limited low FODMAP approach allows for systematic identification of specific triggers and should include: 

• Initial elimination phase (2-6 weeks) 
• Systematic reintroduction protocol testing individual fructan categories 
• Long-term personalized maintenance plan based on tolerance thresholds 

Strategic food modifications 

• Utilize garlic-infused oils (flavor without fructans) 
• Recommend sourdough varieties when appropriate (reduced fructan content through fermentation) 
• Identify suitable low-fructan alternatives (spinach, carrots, tomatoes, kiwi, papaya) 
• Implement portion control strategies for tolerated moderate-fructan foods 
• Consider the timing of fructan intake with digestive capacity 

Microbiome support and diversity  

Research from the American Gut Project shows that consuming 30 or more different plant types per week significantly increases gut microbiome diversity compared to those who eat fewer than 10 plant varieties. Encourage patients to: 

• Maintain plant diversity within their tolerance limits (including fruits, vegetables, grains, nuts, seeds, herbs, and spices). 
• Gradually reintroduce low-fructan prebiotic foods to support beneficial bacteria up to their tolerance.  
• Limit dietary restrictions as much as possible while maintaining symptom control. 

Conclusion 

Recognizing fructan intolerance as a key dietary trigger may shift the clinical conversation beyond gluten and toward more precise, patient-centered care. Applying this knowledge through careful assessment, awareness of diagnostic challenges, and individualized interventions enables dietitians to help with symptom relief while preserving dietary variety and supporting long-term gut health. 

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References

Wilson B, Whelan K. Prebiotic inulin-type fructans and galacto-oligosaccharides: definition, specificity, function, and application in gastrointestinal disorders. J Gastroenterol Hepatol. 2017 Mar;32 Suppl 1:64-68. doi: 10.1111/jgh.13700.  

Biesiekierski JR, Peters SL, Newnham ED, Rosella O, Muir JG, Gibson PR. No Effects of Gluten in Patients With Self-Reported Non-Celiac Gluten Sensitivity After Dietary Reduction of Fermentable, Poorly Absorbed, Short-Chain Carbohydrates. Gastroenterology. 2013;145(2):320-8.e3. 

Skodje GI, Sarna VK, Minelle IH, Rolfsen KL, Muir JG, Gibson PR, et al. Fructan, Rather Than Gluten, Induces Symptoms in Patients With Self-Reported Non-Celiac Gluten Sensitivity. Gastroenterology. 2018;154(3):529-39.e2. 

Nordin E, Brunius C, Landberg R, Hellström PM. FODMAPs, but not gluten, elicit modest symptoms of irritable bowel syndrome: a double-blind, placebo-controlled, randomized three-way crossover trial. The American Journal of Clinical Nutrition. 2021. 

Fedewa A, Rao SS. Dietary fructose intolerance, fructan intolerance and FODMAPs. Curr Gastroenterol Rep. 2014 Jan;16(1):370. doi: 10.1007/s11894-013-0370-0.  

Rhys-Jones, D. (2021, October 28). Gluten and IBS. Monash FODMAP. https://www.monashfodmap.com/blog/gluten-and-ibs/ sciencedirect.com+14monashfodmap.com+14monash  

Collins, L., & RhysJones, D. (2020, June 10). Fructans and FODMAP reintroduction. Monash FODMAP. Retrieved July 3, 2025, from https://www.monashfodmap.com/blog/fructans-fodmap-reintroduction/ 

McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May 15;3(3):e00031-18. doi: 10.1128/mSystems.00031-18.   

Celiac Disease: Fast Facts. Beyond Celiac website. Retrieved October 9, 2025. https://www.beyondceliac.org/celiac-disease/facts-and-figures/